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From Wikipedia:

From 1981 to 1985 Negroponte was the U.S. ambassador to Honduras. During his tenure, he oversaw the growth of military aid to Honduras from $4 million to $77.4 million a year. At the time, Honduras was ruled by an elected but heavily militarily-influenced government. According to The New York Times, Negroponte was allegedly involved in "carrying out the covert strategy of the Reagan administration to crush the Sandinistas government in Nicaragua." Critics say that during his ambassadorship, human rights violations in Honduras became systematic.


Negroponte supervised the construction of the El Aguacate air base where Nicaraguan Contras were trained by the U.S., and which some critics say was used as a secret detention and torture center during the 1980s. In August 2001, excavations at the base discovered 185 corpses, including two Americans, who are thought to have been killed and buried at the site.


Records also show that a special intelligence unit (commonly referred to as a "death squad") of the Honduran armed forces, Battalion 3-16, trained by the CIA and the Argentine military, kidnapped, tortured and killed hundreds of people, including U.S. missionaries. Critics charge that Negroponte knew about these human rights violations and yet continued to collaborate with the Honduran military while lying to Congress.


In May 1982, a nun, Sister Laetitia Bordes, who had worked for ten years in El Salvador, went on a fact-finding delegation to Honduras to investigate the whereabouts of thirty Salvadoran nuns and women of faith who fled to Honduras in 1981 after Archbishop Óscar Romero's assassination. Negroponte claimed the embassy knew nothing. However, in a 1996 interview with the Baltimore Sun, Negroponte's predecessor, Jack Binns, said that a group of Salvadorans, among whom were the women Bordes had been looking for, were captured on April 22, 1981, and savagely tortured by the DNI, the Honduran Secret Police, and then later thrown out of helicopters alive.